Pedigree Reconstruction Using Identity by Descent
Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
Author(s)
Detail(s)
| Original language | English |
|---|---|
| Title of host publication | Research in Computational Molecular Biology |
| Subtitle of host publication | 15th Annual International Conference, RECOMB 2011, Proceedings |
| Editors | Vineet Bafna, S. Cenk Sahinalp |
| Publisher | Springer Verlag |
| Pages | 136-152 |
| ISBN (electronic) | 9783642200366 |
| ISBN (print) | 9783642200359 |
| Publication status | Published - 2011 |
| Externally published | Yes |
Publication series
| Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
|---|---|
| Publisher | Springer |
| Volume | LNBI 6577 |
| ISSN (Print) | 0302-9743 |
| ISSN (electronic) | 1611-3349 |
Conference
| Title | 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011 |
|---|---|
| Place | Canada |
| City | Vancouver, BC |
| Period | 28 - 31 March 2011 |
Link(s)
Abstract
Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very time-consuming and expensive process. Methods for automating the construction of pedigrees could stream-line this process. While constructing single-generation families is relatively easy given whole genome data, reconstructing multi-generational, possibly inbred, pedigrees is much more challenging.
This paper addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This paper introduces two multi-generational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods out-perform the state-of-the-art and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy.
The two programs are available at http://cop.icsi.berkeley.edu/cop/.
This paper addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This paper introduces two multi-generational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods out-perform the state-of-the-art and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy.
The two programs are available at http://cop.icsi.berkeley.edu/cop/.
Citation Format(s)
Pedigree Reconstruction Using Identity by Descent. / Kirkpatrick, Bonnie; Li, Shuai Cheng; Karp, Richard M. et al.
Research in Computational Molecular Biology: 15th Annual International Conference, RECOMB 2011, Proceedings. ed. / Vineet Bafna; S. Cenk Sahinalp. Springer Verlag, 2011. p. 136-152 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. LNBI 6577).
Research in Computational Molecular Biology: 15th Annual International Conference, RECOMB 2011, Proceedings. ed. / Vineet Bafna; S. Cenk Sahinalp. Springer Verlag, 2011. p. 136-152 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. LNBI 6577).
Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
